Remove doubles before export
Running this script will remove doubles on the currently selected mesh and export the file with a filename appended with -unity

You can then set unity to read the -unity blend and run the script instead of save.

import bpy
newfilename = bpy.context.blend_data.filepath.replace(".blend","-unity.blend")
bpy.ops.object.mode_set(mode='EDIT')
bpy.ops.mesh.select_all(action='TOGGLE')
bpy.ops.mesh.remove_doubles()
bpy.ops.wm.save_as_mainfile(copy=True, filepath=newfilename)